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RosettaCommons / PyRosetta.notebooks

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design
https://rosettacommons.github.io/PyRosetta.notebooks/
MIT License
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Why the mutation can not be executed thoroughly? #93

Open JonasLi-19 opened 10 months ago

JonasLi-19 commented 10 months ago

when I use pyrosetta to convert protein amino acid, there is some amino acid keep their original state, some others converted as I commanded.

The function I used is MutateResidue(). As the picture below, the LEU is a converted AA from ASN, but there is still one ASN cannot to be concerted into LEU.

image

roccomoretti commented 10 months ago

It's hard to say without knowing which residue is unable to be mutated, but often the issue is related to the patch state of the residue in question, particularly patches which change the connectivity of the residue.

I would recommend doing a pose.residue(seqpos).name() to see the full name of the residue type at the position which can't change. If it's something like "ASN:CTermProteinFull", the part after the colon is the patch name. When you use MutateResidue, you may have to match the patch state of the residue you're mutating things to (e.g. "LEU:CTermProteinFull").

Dadiao-shuai commented 7 months ago

I want to know if the partial charge be calculated after using amino acid mutation, should I do more work before using the mutated protein for AutoDock4 docking?